Scientific Publications 2006
2006. "ScalaBLAST: A Scalable Implementation of BLAST for High Performance Data-Intensive Bioinformatics Analysis." IEEE Transactions on Parallel and Distributed Systems 17(8):740-749. Abstract Genes in an organism’s DNA (genome) have embedded in them information about proteins, which are the molecules that do most of a cell’s work. A typical bacterial genome contains on the order of 5000 genes. Mammalian genomes can contain hundreds of thousands of genes. For each genome sequenced, the challenge is to identify protein components (proteome) being actively used for a given set of conditions. Fundamentally, sequence alignment is a sequence matching problem focused at unlocking protein information embedded in the genetic code, making it possible to assemble a “tree of life” by comparing new sequences against all sequences from known organisms. But the memory footprint of sequence data is growing more rapidly than per-node core memory. Despite years of research and development, high performance sequence alignment applications either do not scale well, cannot accommodate very large databases in core, or require special hardware. We have developed a high performance sequence alignment application, ScalaBLAST, which accommodates very large databases, and which scales linearly to hundreds of processors on both distributed memory and shared memory architectures, representing a substantial improvement over the current state-of-the-art in high performance sequence alignment with scaling and portability. ScalaBLAST, relies on a collection of innovative techniques -- distributing the target database over available memory, multi-level parallelism to exploit concurrency, parallel I/O, and latency hiding through data prefetching -- to achieve high performance and scalability. This demonstrated approach of database sharing combined with effective task scheduling should have broad ranging applications to other informatics-driven sciences.
2006. "Chemical bonding and electronic structures of the Al2SiO5 polymorphs, andalusite, sillimanite, and kyanite: X-ray photoelectron- and electron energy loss spectroscopy studies." American Mineralogist 91(5-6):740-746. doi:10.2138/am.2006.1887 Abstract We have undertaken a detailed analysis of the X-ray photoelectron spectra obtained from the three polymorphs of Al2SiO5; andalusite, sillimanite, and kyanite. Comparison of the spectra was made based on the chemical bonding and structural differences in the Al- and Si-coordination within each polymorph. The spectra for Si(2p) for all three polymorphs are nearly identical, consistent with the fact that all the Si atoms are in 4-fold (tetrahedral) coordination, whereas the binding energies, peak shapes, and peak widths for Al(2p) vary depending on the type of polymorph. The upper-valence band for all three polymorphs is characterized by four main features derived from O(2p), Al(3s), Al(2p), Si(3s), and Si(3p), and the differences in their contributions are observed. The density of state of the Al2SiO5 polymorphs is relatively featureless compared to those observed from α-SiO2 and α-Al2O3, suggesting that the orbital overlaps span a greater range in energy. The observed band gap energy for Al2SiO5 (sillimanite) was ~9.1eV, a value in between those for α-SiO2 (~8.6eV) and α-Al2O3 (~9.6eV). The conduction band feature of Al2SiO5 was experimentally compared to those of α-SiO2 and α-Al2O3, and shown that it is indeed intermediate between the α-SiO2 and α-Al2O3 phases.
2006. "Corrosion of low level vitrified radioactive waste in a loamy soil." Glass Technology 47(2):48-55. Abstract Corrosion of high sodium borosilicate glass K-26 was examined over 16 years of storage in a loamy soil. An altered layer was formed on the glass surface which is inhomogeneous in thickness and composition. This layer is mostly amorphous with small crystalline inclusions. The pH of the groundwater in contact with the radioactive glass gradually from 7·5 to 7·9 and the groundwater was slightly contaminated with 137Cs at levels from ~20 to below 10 Bq/L after 16 years. The corrosion rate of glass diminishes with time and is 0·22 µg/cm2 day after 16 years.
2006. "A Review of Multidimensional, Multifluid Intermediate-scale Experiments: Nonaqueous Phase Liquid Dissolution and Enhanced Remediation." Vadose Zone Journal 5:570-598. doi:10.2136/vzj2005.0125 Abstract A review is presented of original multidimensional, intermediate-scale experiments involving nonaqueous phase liquids. The experimental approach at this scale can be viewed as an important intermediary between column studies and field trials. The primary advantage of intermediate-scale flow cell experiments is that field-scale processes can be simulated under controlled conditions. The experiments are frequently conducted to provide data sets to test and verify numerical and analytical flow and transport models. The controlled setting and laboratory instrumentation reduces the uncertainty in parameter estimation, allowing comparisons between simulation and experimental results to focus on flow and transport processes. A total of about 120 original contributions were identified and reviewed. Depending on the main topic of NAPL experimental research, the papers were divided into the following sections: (1) Dissolution, (2) Enhanced Remediation, (3) Flow behavior, (4) Quantification, and, (5) Imaging. In this paper, the categories Dissolution and Enhanced Remediation are discussed and suggestions for future research are provided. In a companion paper, experimental work related to the other three categories is reviewed. The Dissolution category includes experiments in which NAPL removal occurs due to water flushing. The Enhanced Remediation section contains experimental contributions investigating surfactant flushing, alcohol flushing, surfactant/alcohol combinations, dense brine barrier strategies, oil recovery through pumping, soil vapor extraction, air sparging, steam injection, bioremediation, and other techniques.
2006. "Behavior of a Viscous LNAPL under Variable Water Table Conditions." Soil & Sediment Contamination 15(6):543 - 564 . doi:10.1080/15320380600958976 Abstract An intermediate-scale experiment in a 1.02-m-long, 0.75-m-high, and 0.05-m-wide flow cell was conducted to investigate the behavior of a viscous LNAPL under variable water table conditions. Two viscous LNAPL volumes (0.4 L) were released, one week apart, from a small source zone on top of the flow cell into a partly saturated, homogenously packed porous medium. Following a redistribution period of 30 days after the second release, the water table was increased 0.5 m in 50 minutes. After the water table rise, viscous LNAPL behavior was monitored for an additional 45 days. Fluid saturation scans were obtained periodically with a fully automated dual-energy gamma radiation system. Results show that both spills follow similar paths downwards. Within two hours after the first LNAPL arrival, the capillary fringe was reduced across the cell by approximately 0.04 m (22%). This reduction is directly related to the decrease in the air-water surface tension from 0.072 to 0.057 N/m. LNAPL drainage from the unsaturated zone was relatively slow and a considerable residual LNAPL saturation was observed after 30 days of drainage. Most of the mobile LNAPL moved into the capillary fringe during this period. After a rapid 0.5 m water table rise, the LNAPL moved up in a delayed fashion. The LNAPL used the same path upwards as it used coming down during the infiltration phase. After 45 days, the LNAPL has moved up only approximately 0.2 m. Since the LNAPL has only moved up a limited amount, nonwetting fluid entrapment was limited. The experiment was simulated using the STOMP multifluid flow simulator, which includes entrapped and residual LNAPL saturation formation. A comparison indicates that the simulator is able to predict the observed phenomena well, including residual saturation formation in the vadose zone, and limited upward LNAPL movement after the water table rise. The results of this experiment show that viscous mobile LNAPL, subject to variable water table conditions, does not necessarily float on the water table and may not appear in an observation well.
2006. "Patterned Regions of Porous Silicon through Trapped Hydrogen Bubbles." Applied Physics Letters 88(14):143113 (3 pages). doi:10.1063/1.2188039 Abstract Hydrogen bubbles trapped around lithographically formed etch pits on silicon single crystal surfaces were used to guide the formation of patterned regions of porous silicon. Optical lithography and wet (electro) chemical etching were utilized in a series of steps to form the etched surface and guide this growth. It was observed that the pits were surrounded by round regions of porous Si suggesting that hydrogen bubbles defined the areas of porous silicon formation. Consistent with earlier results where porosity seemed to form primarily at the bubble edges, a lower overall etch rate was observed near the bubble center. This is consistent with a variable rate of bubble expansion as etching occurred and an ability of the hydrogen to mask or slow the reaction in the bubble center. Contrary to our initial expectations, the surface profile suggested that the region away from the bubbles was also etched, but very uniformly.
2006. "Low Temperature H2O and NO2 Coadsorption on θ-Al2O3/NiAl(100) ultrathin films ." Journal of Physical Chemistry B 110(15):8025-8034. doi:10.1021/jp057534c Abstract The co-adsorption of H2O and NO2 molecules on a well-ordered, ultrathin θ-Al2O3/NiAl(100) film surface was studied using temperature programmed desorption (TPD), infrared reflection absorption spectroscopy (IRAS) and X-ray photoelectron spectroscopy (XPS). For H2O and NO2 monolayers adsorbed separately on the θ-Al2O3/NiAl(100) surface, adsorption energies were estimated to be 44.8 kJ/mol and 36.6 kJ/mol, respectively. Coadsorption systems prepared by sequential deposition of NO2 and H2O revealed the existence of coverage and temperature dependent adsorption regimes where H2O molecules and the surface NOx species (NO2/N2O4/NO2-,NO3-) form segregated and/or mixed domains. Influence of the changes in the crystallinity of solid water (amorphous vs. crystalline) on the coadsorption properties of the NO2/H2O/θ-Al2O3/NiAl(100) system is also discussed.
2006. "Model NOx storage systems: Storage capacity and thermal aging of BaO/theta- Al2O3/NiAl(100)." Journal of Catalysis 243(1):149-157. doi:10.1016/j.jcat.2006.06.028 Abstract The NO;( storage properties of a BaO/θ-AlO/NiAl(100) model system, with a BaO coverage of ∼2 monolayer equivalent (MLE), was studied. X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD) techniques were used to investigate NO adsorption and reaction on the BaO/θ-AlO/NiAl(100) surface. These results were compared with those of the θ-AlO/NiAl(100) support material, a thermally aged BaO/θ-AlO/NiAl(100) model system, and a realistic BaO (20 wt%)/γ-AlO high-surface area counterpart. At T > 300 K, adsorbed NO is converted to nitrates on all of the surfaces studied. Nitrates residing on the alumina sites of the model catalyst surfaces are relatively weakly bound and typically desorb within 300-600 K, leading to NO(g) evolution; while nitrates associated with the baria sites are significantly more stable and desorb within 600-850 K, resulting in NO(g) or NO(g) + O(g) evolution. NO[x] uptake by the baria sites of the BaO/θ-AlO/NiAl(100) model system was found to be as much as five-fold greater than that of the θ-AlO/NiAl(100) support material. Thermal aging of a BaO/0-AlO/NiAl(100) surface at 1100 K before NO[x] uptake experiments brings about a significant (>70%) reduction in the NO[x] storage capacity of the model catalyst surface.